segmasker

name	segmasker
description	Use when identifying and masking low-complexity regions in protein sequences with the SEG algorithm before BLAST or other downstream analyses.
disable-model-invocation	true
user-invocable	true

segmasker

Quick Start

• Command: segmasker
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/segmasker
• Version: BLAST+ 2.17.0+
• Full reference: See references/help.md

When To Use This Tool

• Mask low-complexity regions in protein sequences before blastp, rpsblast, or related protein-domain searches.
• Emit interval masks, masked FASTA, or ASN.1/XML mask metadata for downstream tooling.
• Prepare masking information from FASTA or an existing protein BLAST database.
• Prefer dustmasker for nucleotide low-complexity masking.

Common Patterns

# 1) Produce interval-style SEG mask coordinates
segmasker \
  -in proteins.fa \
  -out proteins.seg.interval \
  -outfmt interval

# 2) Emit masked FASTA for downstream protein BLAST
segmasker \
  -in proteins.fa \
  -out proteins.masked.fa \
  -outfmt fasta

# 3) Tune SEG aggressiveness
segmasker \
  -in proteins.fa \
  -out proteins.masked.fa \
  -outfmt fasta \
  -window 12 \
  -locut 2.2 \
  -hicut 2.5

Recommended Workflow

1. Decide whether downstream tools want coordinates, masked FASTA, or mask metadata.
2. Run with default SEG parameters first; tune -window, -locut, and -hicut only if masking is obviously too weak or too strong.
3. Inspect the masked output before pushing it into alignment or search workflows.
4. Keep the unmasked protein FASTA alongside the masked output for traceability.

Guardrails

• segmasker is the protein low-complexity masker; use dustmasker for nucleotide data.
• The default output format is interval, not FASTA.
• There is no separate hard-masking switch here; choose the output format that your downstream tool expects.
• If FASTA identifiers matter downstream, consider -parse_seqids.